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Deep‐sea chemosynthetic ecosystems are 'oases' of life powered by reducing geofluids, of which serpentinite‐hosted seeps are among the least studied. South Chamorro Seamount, a serpentine mud volcano on the Mariana Arc, has been known to host chemosynthesis‐based assemblages since 1996, but no detailed information on the fauna was published. Here, we revisited South Chamorro to characterise its biodiversity. We located two regions of chemosynthetic communities dominated by bathymodioline mussels, vesicomyid clams, and chaetopterid parchment worms: one on the northwestern flank ('Fryer Site') and one on the southern summit ('Summit Site'). We sampled a total of 20 species including 13 molluscs, five annelids, and two crustaceans – all present on the more active Summit Site but only a subset being found at Fryer Site. A mussel bed surrounding the Fryer Site was drilled by the Ocean Drilling Program in 2001 resulting in six holes, the deepest being 266 m (Hole 1200C). Cuttings ~50 cm deep still cover an approximately 60 m radius around Hole 1200C even 22 years later, and there is no sign of recovery. Low geofluid supply in serpentinite‐hosted seamounts may not allow decadal recovery of animal colonies, unlike a previous drilling site in an Okinawa Trough vent. [ABSTRACT FROM AUTHOR]

Chemosynthetic ecosystems powered by microbial primary production are rare 'hot spots' of biological activity in the deep‐sea characterized by dense aggregations of specially adapted animal species. Among settings where such systems have been found, serpentinite‐hosted seep systems supported by alkaline geofluid are particularly understudied with just a few known sites worldwide. Mariana Forearc hosts the world's only series of active serpentinite mud volcanoes, but seep communities have only been reported from South Chamorro Seamount where large bathymodioline mussels dominate. Here, we report the discovery of a serpentinite‐hosted seep on the conical summit of Asùt Tesoru Seamount, Mariana Forearc. Named the 'Big Blue Seep', this field features white, likely carbonate crusts inhabited by animals, under which fluid seepage could be seen. We confirm 16 animal species, including typical seep‐associated fauna such as Desbruyeresia gastropods and Acharax awning‐clams. This is surprising as previous research expeditions did not notice any sign of chemosynthesis‐based ecosystems on this seamount, although the community is indeed difficult to spot due to the lack of large‐bodied epifauna such as mussels. The Big Blue Seep is adjacent to three drill holes made by the International Ocean Discovery Program expedition 366 (Holes U1496A‐C), which may have impact on seepage. Our findings represent the second chemosynthesis‐based ecosystem associated with serpentinite mud volcanism, suggestive of further such communities on other Mariana Forearc mud volcanoes. [ABSTRACT FROM AUTHOR]

The Capitanian stage is characterized by marine anoxia possibly related to the extinction, although the global redox structure of the Capitanian ocean has not been constrained. We newly report a nitrogen isotope (δ15N) record from a paleo‐atoll limestone at the top of a mid‐Panthalassan seamount to constrain the spatial extent and duration of the Capitanian marine anoxia. The δ15N value of limestone after acid treatment is substantially high for ∼5‐Myr up to +28‰, the highest through the Phanerozoic oceans, suggesting that the nitrogen source (nitrate) was substantially enriched in 15N via denitrification within subsurface oxygen‐deficient zones (ODZs; O2 < 5 µM). Numerical modeling of nitrogen isotope dynamics in the upwelling system along the seamount suggests that the possible minimum δ15N value of a global deep‐oceanic nitrate reservoir was ca. +9‰ in the Capitanian (∼4‰ higher than at the present). Furthermore, a redox‐dependent nitrogen isotope mass balance model constrained the global redox structure of the Capitanian superocean. Substantially reducing conditions (O2 ≤ 20 µM) prevailed at intermediate water depths (100–1,000 m), in association with expanded ODZs with anoxic/euxinic cores along continental margins (≥ ∼0.4% of global ocean volume), while the deep‐ocean remained to be more oxidizing (O2 ≤ 60 µM). The enhanced open‐ocean productivity associated with the low sea‐level and high nutrient flux to the ocean resulted in the global ocean deoxygenation during the cooling stage. Our model is consistent with previous geologic observations and with a possible link between the long‐term (∼5‐Myr) development of marine dysoxia and the extinction. Plain Language Summary: The Capitanian stage is a peculiar stage characterized by several environmental changes including marine anoxia, possibly related to the large extinction. Previous studies reported the evidence for marine anoxia developed at least locally in the Capitanian, although the spatial extent and duration of anoxia in the superocean Panthalassa in the stage have been poorly constrained. Bioavailable nitrogen is essential for life and the nitrogen isotopic composition of sedimentary record is useful to reconstruct the global nitrogen cycle in association with oceanic redox condition in the past. We report a ∼5‐Myr‐long nitrogen isotope record from a shallow‐water limestone in the lost mid‐superocean during the Capitanian. This unique record reveals major changes in global nitrogen cycle in the stage, that is, the appearance of a substantially 15N‐enriched oceanic nitrate reservoir indicating enhanced anaerobic respiration under reducing conditions. Numerical modeling further constrains that the reducing water masses (O2 < 20 μM) prevailed at intermediate water depths (100–1,000 m) in the superocean, in association with the expanded oxygen‐deficient zones with anoxic/euxinic cores developed along the continental margins (at least twice as much as in the modern oceans). Our new model is consistent with the scenario that the long‐term subsurface anoxia/euxinia contributed to the shelf extinction. Key Points: N isotope record from the mid‐Panthalassa suggesting expanded oxygen‐deficient zones in mid‐water depths (>∼0.4% of global ocean volume)Substantially reducing ocean in association with the low sea‐level, high nutrient flux to the ocean, and enhanced open‐ocean productivityA possible link between the long‐term (∼5‐Myr) deep‐water anoxia/euxinia along the continental margins and the shelf extinction [ABSTRACT FROM AUTHOR]

Lakes of molten sulfur are features sometimes found in seafloor hydrothermal vent systems. Daikoku of the northern Mariana Arc is notable for being home to one of such features inside its summit caldera, the "Sulfur Cauldron" discovered in 2006. A number of oceanographic research cruises since then have revealed significant volcanic activities on Daikoku Seamount, including an eruption event in 2014 leading to the formation of a new basin‐like crater. How this event impacted the sulfur lake on Daikoku Seamount remained unclear. Here, we revisited Daikoku Seamount with a remotely operated vehicle to show that the new crater is currently home to a much larger molten sulfur lake than the Sulfur Cauldron, which we name the "Rengoku" sulfur lake. Our samples provided new insights on the structure of submarine sulfur lakes, and contribute to the time‐series observation of volcanic and hydrothermal activities on Daikoku Seamount. [ABSTRACT FROM AUTHOR]

H2‐rich ultramafic‐hosted hydrothermal systems are considered to be important places for the origin and early evolution of life. In this study, we conducted two hydrothermal serpentinization/carbonation experiments involving synthetic komatiite under CO2‐rich conditions to further understand the chemical nature of hydrothermal fluids in the komatiite‐hosted seafloor hydrothermal systems in the early Earth. The H2 concentration in fluid at 300°C is one order of magnitude lower than that under CO2‐free conditions, which revealed that the carbonation of komatiites suppressed H2 generation under CO2‐rich conditions. The steady‐state H2 concentrations in the fluid increased with increasing temperature, while the Fe content of carbonate minerals in the run products increased with decreasing temperature. This correlation suggested that Fe incorporation into the carbonate minerals would limit the H2 generation during the serpentinization of komatiites at each temperature. In addition, the pH of the fluid also depended on temperature. High‐temperature (>300°C) fluids became alkaline, whereas low‐temperature fluids became acidic. Thermodynamic calculations show that the acidic fluids were attributed to high water/rock ratio during the hydrothermal reactions. Consequently, H2‐poor and acidic fluids were likely generated at low temperatures. In contrast, the H2‐rich and alkaline hydrothermal fluids were generated at temperatures above 300°C, which suggests that high‐temperature seafloor hydrothermal systems may be more favorable than lower‐temperature systems for the emergence and early evolution of life in the Hadean ocean in terms of the formation of energy and electrochemical potentials between hydrothermal fluids and ambient seawater. Key Points: Fe incorporation into the carbonate minerals limits the H2 generation during serpentinizationHigh‐temperature seafloor hydrothermal systems may be favorable for the emergence and early evolution of lifeThe H2 flux from serpentinization in the Archean would be much lower than that at present [ABSTRACT FROM AUTHOR]

Seafloor cratering is an important process that records the impact history of the Earth, affects projectile survivability, and determines the mass of ejecta from benthic rock that is transported to the atmosphere. We report experimental hypervelocity impacts of chondrite and other projectiles (olivine, stainless‐steel, polycarbonate) on a water‐covered iron target to derive a scaling relationship for benthic cratering. In situ observations of 5‐km/s impacts quantify the deceleration of projectiles in the water column by shock‐induced deformation and fragmentation. The minimum water depths at which multiple craters appeared on the benthic target were two and four times the projectile diameter for chondrite and stainless steel, respectively. Based on the observed deceleration of projectiles in water, the cratering efficiency of a benthic target for a given impact velocity is predicted to follow an exponential decay law in terms of water depth normalized by projectile diameter (H/d), given by πv ∝ exp(−(H/d)/κ), when a projectile of original mass collides with the target. Comparing the volume of the largest crater in the experiments and that derived from the scaling relation, mass ratios of the largest projectile fragment to original projectile in the 5‐km/s impact were calculated to be 0.1–0.3 (H/d = 2–6) and 1.0 ± 0.3 (H/d = 5.5) for chondrite and stainless steel, respectively. Using the scaling relationship, the volume of the transient crater on oceanic crust by an asteroid impact is estimated to be smaller than previously predicted by hydrocode simulation when the asteroid fragmentation in the water column controls seafloor cratering. Plain Language Summary: The hypervelocity (measured in km/s) impact of extraterrestrial bodies in the marine environment is more common than that on land because ∼70% of the Earth's surface is covered by oceans. Seafloor cratering is important for recording Earth's impact history, driving environmental, biotic, and climatic perturbations by ejecting crustal materials into the atmosphere (e.g., the K‐T boundary event); impactors can also affect the fate of extraterrestrial organic matter and may have been key components of primitive life on early Earth (the so‐called panspermia hypothesis). Herein, we simulated the oceanic hypervelocity impacts of asteroids in a laboratory to derive a scaling relationship for benthic cratering. Our results suggest that deformation and fragmentation of projectiles occurs during the impact penetration of water at an initial impact velocity of 5 km/s, thereby controlling the water depth conditions that enable benthic cratering. The experimentally derived scaling relationship of benthic cratering permits the estimation of transient crater volume of oceanic crust in a given water depth by a chondrite impact. Key Points: Oceanic hypervelocity impacts of asteroids were simulated in a laboratory settingDeformation and fragmentation of projectiles within the water column controlled benthic crateringBased on the experimental data, a scaling relation for benthic cratering is provided [ABSTRACT FROM AUTHOR]

Studying the diversity of extant metabolisms and enzymes, especially those involved in the biosynthesis of primary metabolites including amino acids, is important to shed light on the evolution of life. Many organisms synthesize serine from phosphoserine via a reaction catalyzed by phosphoserine phosphatase (PSP). Two types of PSP, belonging to distinct protein superfamilies, have been reported. Genomic analyses have revealed that the thermophilic bacterium Thermus thermophilus lacks both homologs while still having the ability to synthesize serine. Here, we purified a protein from T. thermophilus which we biochemically identified as a PSP. A knockout mutant of the responsible gene (TT_C1695) was constructed, which showed serine auxotrophy. These results indicated the involvement of this gene in serine biosynthesis in T. thermophilus. TT_C1695 was originally annotated as a protein with unknown function belonging to the haloacid dehalogenase‐like hydrolase (HAD) superfamily. The HAD superfamily, which comprises phosphatases against a variety of substrates, includes also the classical PSP as a member. However, the amino acid sequence of the TT_C1695 was more similar to phosphatases acting on non‐phosphoserine substrates than classical PSP; therefore, a BLASTP search and phylogenetic analysis failed to predict TT_C1695 as a PSP. Our results strongly suggest that the T. thermophilus PSP and classical PSP evolved specificity for phosphoserine independently. Enzymes: Phosphoserine phosphatase (PSP; EC 3.1.3.3); serine hydroxymethyltransferase (EC 2.1.2.1); 3‐phosphoglycerate dehydrogenase (EC 1.1.1.95); 3‐phosphoserine aminotransferase (EC 2.6.1.52). The serine biosynthetic pathway for the thermophilic bacterium Thermus thermophilus was previously unknown and phosphoserine phosphatase (PSP), an enzyme necessary for the pathway, had not been identified. Here, we identified a novel PSP in T. thermophilus belonging to the same protein superfamily as classical PSPs. However, these two types of PSP are likely to have independently evolved specificity for phosphoserine. [ABSTRACT FROM AUTHOR]

Summary: Various lineages of ammonia‐oxidizing archaea (AOA) are present in deep waters, but the mechanisms that determine ecotype formation are obscure. We studied 18 high‐quality genomes of the marine group I AOA lineages (alpha, gamma and delta) from the Mariana and Ogasawara trenches. The genomes of alpha AOA resembled each other, while those of gamma and delta lineages were more divergent and had even undergone insertion of some phage genes. The instability of the gamma and delta AOA genomes could be partially due to the loss of DNA polymerase B (polB) and methyladenine DNA glycosylase (tag) genes responsible for the repair of point mutations. The alpha AOA genomes harbour genes encoding a thrombospondin‐like outer membrane structure that probably serves as a barrier to gene flow. Moreover, the gamma and alpha AOA lineages rely on vitamin B12‐independent MetE and B12‐dependent MetH, respectively, for methionine synthesis. The delta AOA genome contains genes involved in uptake of sugar and peptide perhaps for heterotrophic lifestyle. Our study provides insights into co‐occurrence of cladogenesis and anagenesis in the formation of AOA ecotypes that perform differently in nitrogen and carbon cycling in dark oceans. [ABSTRACT FROM AUTHOR]

The study of extracellular DNA viral particles in the ocean is currently one of the most advanced fields of research in viral metagenomic analysis. However, even though the intracellular viruses of marine microorganisms might be the major source of extracellular virus particles in the ocean, the diversity of these intracellular viruses is not well understood. Here, our newly developed method, referred to herein as fragmented and primer ligated dsRNA sequencing (flds) version 2, identified considerable genetic diversity of marine RNA viruses in cell fractions obtained from surface seawater. The RNA virus community appears to cover genome sequences related to more than half of the established positive‐sense ssRNA and dsRNA virus families, in addition to a number of unidentified viral lineages, and such diversity had not been previously observed in floating viral particles. In this study, more dsRNA viral contigs were detected in host cells than in extracellular viral particles. This illustrates the magnitude of the previously unknown marine RNA virus population in cell fractions, which has only been partially assessed by cellular metatranscriptomics and not by contemporary viral metagenomic studies. These results reveal the importance of studying cell fractions to illuminate the full spectrum of viral diversity on Earth. [ABSTRACT FROM AUTHOR]

Abstract: Deep‐sea hydrothermal vents are hot springs on the seafloor. In recent years, electricity generation in deep‐sea hydrothermal vents has been reported. Electricity can be generated through the sulfide minerals that form in seafloor hydrothermal deposits, and these minerals can convert the redox and heat energy between hydrothermal fluids and seawater into electric power. The physical and chemical phenomena of generating electricity from natural minerals provide key insights into development of deep‐sea power plants and novel electricity‐conversion materials with earth abundant elements. In addition, the new findings have established a novel concept of life, e. g., existence of electricity‐sustained life in hydrothermal vents and widespread occurrence of electron‐uptake ecosystems on the seafloor, together with a new hypothesis about the origin of life. [ABSTRACT FROM AUTHOR]

Deep-sea hydrothermal vents discharge abundant reductive energy into oxidative seawater. Herein, we demonstrated that in situ measurements of redox potentials on the surfaces of active hydrothermal mineral deposits were more negative than the surrounding seawater potential, driving electrical current generation. We also demonstrated that negative potentials in the surface of minerals were widespread in the hydrothermal fields, regardless of the proximity to hydrothermal fluid discharges. Lab experiments verified that the negative potential of the mineral surface was induced by a distant electron transfer from the hydrothermal fluid through the metallic and catalytic properties of minerals. These results indicate that electric current is spontaneously and widely generated in natural mineral deposits in deep-sea hydrothermal fields. Our discovery provides important insights into the microbial communities that are supported by extracellular electron transfer and the prebiotic chemical and metabolic evolution of the ocean hydrothermal systems. [ABSTRACT FROM AUTHOR]

Subseafloor pelagic sediments with high concentrations of organic matter form habitats for diverse microorganisms. Here, we determined depth profiles of genes for SSU rRNA, mcrA, dsrA and amoA from just beneath the seafloor to 363.3 m below the seafloor (mbsf) using core samples obtained from the forearc basin off the Shimokita Peninsula. The molecular profiles were combined with data on lithostratigraphy, depositional age, sedimentation rate and pore-water chemistry. The SSU rRNA gene tag structure and diversity changed at around the sulfate-methane transition zone ( SMTZ), whereas the profiles varied further with depth below the SMTZ, probably in connection with the variation in pore-water chemistry. The depth profiles of diversity and abundance of dsrA, a key gene for sulfate reduction, suggested the possible niche separations of sulfate-reducing populations, even below the SMTZ. The diversity and abundance patterns of mcrA, a key gene for methanogenesis/anaerobic methanotrophy, suggested a stratified distribution and separation of anaerobic methanotrophy and hydrogenotrophic or methylotrophic methanogensis below the SMTZ. This study provides novel insights into the relationships between the composition and function of microbial communities and the chemical environment in the nutrient-rich continental margin subseafloor sediments, which may result in niche separation and variability in subseafloor microbial populations. [ABSTRACT FROM AUTHOR]

Current high-performance thermoelectric materials require elaborate doping and synthesis procedures, particularly in regard to the artificial structure, and the underlying thermoelectric mechanisms are still poorly understood. Here, we report that a natural chalcopyrite mineral, Cu1+xFe1−xS2, obtained from a deep-sea hydrothermal vent can directly generate thermoelectricity. The resistivity displayed an excellent semiconducting character, and a large thermoelectric power and high power factor were found in the low x region. Notably, electron-magnon scattering and a large effective mass was detected in this region, thus suggesting that the strong coupling of doped carriers and antiferromagnetic spins resulted in the natural enhancement of thermoelectric properties during mineralization reactions. The present findings demonstrate the feasibility of thermoelectric energy generation and electron/hole carrier modulation with natural materials that are abundant in the Earth's crust. [ABSTRACT FROM AUTHOR]

There has been much progress in understanding the nitrogen cycle in oceanic waters including the recent identification of ammonia-oxidizing archaea and anaerobic ammonia oxidizing (anammox) bacteria, and in the comprehensive estimation in abundance and activity of these microbial populations. However, compared with the nitrogen cycle in oceanic waters, there are fewer studies concerning the oceanic benthic nitrogen cycle. To further elucidate the dynamic nitrogen cycle in deep-sea sediments, a sediment core obtained from the Ogasawara Trench at a water depth of 9760 m was analysed in this study. The profiles obtained for the pore-water chemistry, and nitrogen and oxygen stable isotopic compositions of pore-water nitrate in the hadopelagic sediments could not be explained by the depth segregation of nitrifiers and nitrate reducers, suggesting the co-occurrence of nitrification and nitrate reduction in the shallowest nitrate reduction zone. The abundance of SSU r RNA and functional genes related to nitrification and denitrification are consistent with the co-occurrence of nitrification and nitrate reduction observed in the geochemical analyses. This study presents the first example of cooperation between aerobic and anaerobic nitrogen metabolism in the deep-sea sedimentary environments. [ABSTRACT FROM AUTHOR]

Tiefseechemie: Die elektrochemische Analyse hydrothermaler Flüssigkeiten und des umgebenden Meerwassers mit Brennstoffzellen, die in hydrothermalen Tiefseespalten installiert wurden, lieferte Hinweise auf die Möglichkeit zur Erzeugung von Elektrizität in der Tiefsee. Das Aufleuchten von Leuchtdioden in der dunklen Umgebung (siehe Bild) bestätigte dies ebenfalls. [ABSTRACT FROM AUTHOR]

Sulfur budgets and seasonal progression of sulfur cycling processes were investigated in Lake Fukami-ike, a small monomictic lake in Japan. The sulfur isotopic mass balance shows that the main sulfur source is groundwater inflow (δ34S = -15.0‰. The sulfate influx is approximately 20% reduced by microbial sulfate reduction and deposited as sulfide (δ34S = -22.2‰ 34 kmol yr-1); the remaining exits from the outflow channel (δ34S = -12.6‰. In the water column, microbiological analyses reveal that green sulfur bacteria dominate more than 90% of the population in the anoxic layer. A monthly decrease in sulfate concentration at each depth indicates that sulfate reduction proceeds within the water column as a first-order reaction because of low sulfate concentration (< 600 µmol L-1). The isotopic fractionation factor of sulfate reduction is estimated to be 0.980 by the isotopic and concentration data of sulfate and sulfide from April to August. Numerical simulation indicates that the relative contribution of phototrophic sulfide oxidation is over 50 times slower than sulfate reduction from April to August but over two times higher from October to November because of lower sulfate conditions (< 300 µmol L-1). Sulfate concentration is the factor for controlling the relative contribution of sulfate reduction and phototrophic sulfide oxidation in monomictic lakes, which contrasts with that observed in permanently stratified lakes. [ABSTRACT FROM AUTHOR]

Summary Domain-level identification of microbial cells or cell-like structures is crucial for investigating natural microbial communities and their ecological significance. By using micro-Fourier transform infrared (micro-FTIR) spectroscopy, we established a technical basis for the domain-level diagnosis and quantification of prokaryotic cell abundance in natural microbial communities. Various prokaryotic cultures (12 species of bacteria and 10 of archaea) were examined using micro-FTIR spectroscopic analysis. The aliphatic CH3/CH2 absorbance ratios ( R3/2) showed domain-specific signatures, possibly reflecting distinctive cellular lipid compositions. The signatures were preserved even after chemical cell fixation (formaldehyde) and nucleic acid staining (DAPI) processes - techniques that are essential in studying microbial ecology. The micro-FTIR technique was successfully applied for quantification of the bacteria/archaea abundance ratio in an active microbial mat community in a subsurface hot aquifer stream. We conclude that the micro-FTIR R3/2 measurement is both fast and effective for domain-level diagnosis and quantification of first-order prokaryotic community structures. [ABSTRACT FROM AUTHOR]

The molecular components involved in energy metabolism of deep-sea Epsilonproteobacteria were characterized in the mesophilic hydrogen- and sulfur-oxidizing chemolithoautotroph Sulfurovum sp. NBC37-1. Previous whole-genome analysis of strain NBC37-1 identified key genes likely to be associated with both sulfur reduction ( psr gene families) and oxidation (two sox gene clusters). However, the sox gene clusters showed unique organizations and low homologies to those in other bacteria. Therefore, the biochemical mechanism of inorganic sulfur metabolism has been uncertain. Enzymatic activity measurements and partial protein purification indicated that the Sox enzyme system was constitutively expressed, whereas the expression of sulfur-reduction enzymes varied depending on the culture conditions. The operative Sox system in strain NBC37-1 required membrane components. The molecular basis of energy metabolism reported in this study provides important insight into how deep-sea Epsilonproteobacteria change their energy metabolism in response to variable physical and chemical conditions in mixing zones between hydrothermal fluid and ambient seawater. [ABSTRACT FROM AUTHOR]

Two novel, thermophilic piezophiles, capable of chemolithoautotrophic growth, are successfully cultivated and isolated from a black smoker chimney at the TAG field (Mid Atlantic Ridge: MAR) by using a piezophilic cultivation technique. Both strains (strains 106 and 108) represent dominant cultivated populations of the microbial communities in the chimney surface habitat. Strain 106 represents typically thin, long spiral cells under the piezophilic growth condition but short bent cells under the non-piezophilic condition. It is a strictly chemolithoautotrophic gammaproteobacterium using reduced sulfur compounds as the electron donors, and nitrate and O2 as the electron acceptors. Based on the 16S rRNA gene sequence, strain 106 would represent a novel genus of the previously uncultivated group (Symbiont Group I; a potentially novel family) within the Gammaproteobacteria, and ‘ Thioprofundum lithotrophica’ gen. nov., sp. nov. is proposed. Strain 108 is a short, oval rod at any of the growth pressures. It is a facultative chemoautotroph, capable of both chemolithoautotrophic growth with H2 and S oxidations and organotrophic growth with complex organics or organic acids using nitrate and O2 as the electron acceptors. The chemolithoautotrophic growth is strictly piezophilic and under the organotrophic growth condition, it grows at conventional pressures (0.1 MPa). Strain 108 is phylogenetically distinctive from any of the previously described genera of the family Rhodobacteraceae within the Alphaproteobacteria, and ‘ Piezobacter thermophilus’ gen. nov., sp. nov. is proposed. The piezophilic cultivation technique can be a powerful tool to isolate and characterize the previously uncultivated phylotypes in the deep-sea hydrothermal vent environments. [ABSTRACT FROM AUTHOR]

Culture-dependent and independent methods were used to evaluate the microbial communities in cores collected at depths up to 200 m in oil-bearing and oil-free strata near the Sagara oil reservoir near Shizuoka, Japan. Direct microbial counts revealed much higher numbers (2.2 × 104-7.9 × 106/g) of microbes in the oil-bearing strata than in the oil-free zones, where counts were uniform at approximately 1.0 × 104/g. Molecular taxonomic analyses via 16S rRNA gene sequence comparisons showed that the oil-free strata were dominated by members of the γ-Proteobacteria including Pseudomonas, Stenotrophomonas and Sphingomonas, whereas the oil-bearing strata were dominated by a single species closely related to Pseudomonas stutzeri. All archaeal clones were phylogenetically affiliated with the uncultured soil group in Crenarchaeota with the exception of a single phylotype that belonged to the genus Thermococcus. Culture-dependent analysis was carried out by most-probable-number culturing as well as direct plating to determine viable cell counts, using both complex organic substrates or native oil and autotrophic media. Both culture-dependent and independent methods revealed the abundant cultivable member was the aerobic oil-degrading bacterium Pseudomonas stutzeri and neither autotrophs nor anaerobic heterotrophs could be detected in the oil-bearing strata. [ABSTRACT FROM AUTHOR]

Novel hydrothermal activities accompanying effluent white smokers and elemental sulfur chimney structures at the north-east lava dome of the TOTO caldera depression in the Mariana Volcanic Arc have been explored and characterized by geochemical and microbiological surveys. White smoker hydrothermal fluids were observed in the potential hydrothermal activity centre of the field and represented the maximal temperature of 170°C and the lowest pH of 1.6. The chimney structures, all consisting of elemental sulfur (sulfur chimney), were also unique to the TOTO caldera hydrothermal field. Microbial community structures in a sulfur chimney and its formation hydrothermal fluid with a high concentration of hydrogen sulfide (15 mM) have been investigated by culture-dependent and -independent analyses. 16S rRNA gene clone analysis and fluorescence in situ hybridization (FISH) analysis revealed that ℇ- Proteobacteria dominated the microbial communities in the sulfur chimney structure and formed a dense microbial mat covering the sulfur chimney surface. Archaeal phylotypes were consistently minor components in the communities and related to the genera Thermococcus, Pyrodictium, Aeropyrum, and the uncultivated archaeal group of ‘deep-sea hydrothermal vent euryarchaeotal group’. Cultivation analysis suggested that the chemolithoautotrophs might play a significant ecological role as primary producers utilizing gas and sulfur compounds provided from hydrothermal fluids. [ABSTRACT FROM AUTHOR]

A multilevel sampler (MLS) was emplaced in a borehole straddling anaerobic, sulfate-rich Cretaceous-era shale and sandstone rock formations ∼200 m below ground surface at Cerro Negro, New Mexico. Sterile quartzite sand contained in chambers in the sampler allowed in situ colonization and recovery of nucleic acids for molecular analyses. Denaturing gradient gel electrophoresis and 16S rRNA gene cloning results indicated a homogeneously distributed bacterial community across the shale–sandstone interface. δ-Proteobacteria sequences were common at all depths, and were dominated by members of the Geobacteraceae family ( Pelobacter, Desulphuromonas and Geobacter). Other members of this group are capable of dissimilatory Fe(III) and/or S° reduction, but not sulfate reduction. RNA hybridization data also suggested that Fe(III)-/S°-reducing bacteria were predominant. These findings are striking considering the lack of significant concentrations of these electron acceptors in this environment. The next most abundant bacterial group indicated was the sulfate reducers, including Desulfobacterium, Desulfocapsa and Desulfobulbus. Sequences related to fermenters, denitrifiers and acetogens were also recovered. The presence of a phylogenetically and functionally diverse microbial community in this deep subsurface environment likely reflects the complex nature of the primary energy and carbon sources, kerogen associated with the shale. [ABSTRACT FROM AUTHOR]

Within a phylum Crenarchaeota, only some members of the hyperthermophilic class Thermoprotei, have been cultivated and characterized. In this study, we have constructed a metagenomic library from a microbial mat formation in a subsurface hot water stream of the Hishikari gold mine, Japan, and sequenced genome fragments of two different phylogroups of uncultivated thermophilic Crenarchaeota: (i) hot water crenarchaeotic group (HWCG) I (41.2 kb), and (ii) HWCG III (49.3 kb). The genome fragment of HWCG I contained a 16S rRNA gene, two tRNA genes and 35 genes encoding proteins but no 23S rRNA gene. Among the genes encoding proteins, several genes for putative aerobic-type carbon monoxide dehydrogenase represented a potential clue with regard to the yet unknown metabolism of HWCG I Archaea. The genome fragment of HWCG III contained a 16S/23S rRNA operon and 44 genes encoding proteins. In the 23S rRNA gene, we detected a homing-endonuclease encoding a group I intron similar to those detected in hyperthermophilic Crenarchaeota and Bacteria, as well as eukaryotic organelles. The reconstructed phylogenetic tree based on the 23S rRNA gene sequence reinforced the intermediate phylogenetic affiliation of HWCG III bridging the hyperthermophilic and non-thermophilic uncultivated Crenarchaeota. [ABSTRACT FROM AUTHOR]

Epsilon- Proteobacteria is increasingly recognized as an ecologically significant group of bacteria, particularly in deep-sea hydrothermal environments. In this study, we studied the spatial distribution, diversity and physiological characteristics of the epsilon- Proteobacteria in various microbial habitats in the vicinity of a deep-sea hydrothermal vent occurring in the Iheya North field in the Mid-Okinawa Trough, by using culture-dependent and -independent approaches. The habitats studied were inside and outside hydrothermal plume, and annelid polychaete tubes. In addition, we deployed colonization devices near the vent emission. The polychaete tubes harboured physiologically and phylogenetically diverse microbial community. The in situ samplers were predominantly colonized by epsilon -Proteobacteria. Energy metabolism of epsilon- Proteobacteria isolates was highly versatile. Tree topology generated from the metabolic traits was significantly different ( P = 0.000) from that of 16S rRNA tree, indicating current 16S rRNA gene-based analyses do not provide sufficient information to infer the physiological characteristics of epsilon- Proteobacteria. Nevertheless, culturability of epsilon- Proteobacteria in various microbial habitats differed among the phylogenetic subgroups. Members of Sulfurimonas were characterized by the robust culturability, and the other phylogenetic subgroups appeared to lose culturability in seawater, probably because of the sensitivity to oxygen. These results provide new insight into the ecophysiological characteristics of the deep-sea hydrothermal vent epsilon- Proteobacteria, which has never been assessed by comparative analysis of the 16S rRNA genes. [ABSTRACT FROM AUTHOR]

Summary Subsurface microbial community structure in relation to geochemical gradients and lithology was investigated using a combination of molecular phylogenetic and geochemical analyses. Discreet groundwater and substratum samples were obtained from depths ranging from 182 to 190 m beneath the surface at approximately 10-cm intervals using a multilevel sampler (MLS) that straddled Cretaceous shale and sandstone formations at a site in the southern San Juan Basin in New Mexico. DNA and RNA were extracted directly from quartzite sand substratum loaded into individual cells of the MLS and colonized in situ . Polymerase chain reaction (PCR)-mediated T-RFLP analysis of archaeal rRNA genes (rDNA) in conjunction with partial sequencing analysis of archaeal rDNA libraries and quantitative RNA hybridization with oligonucleotide probes were used to probe community structure and function. Although total microbial populations remained relatively constant over the entire depth interval sampled, significant shifts in archaeal populations, predominantly methanogens, were observed. These shifts coincided with the geochemical transition from relatively high methane (26 mM), low sulphate (< 3 mg l-1 ) conditions in the region adjacent to the organic matter-rich shale to relatively low-methane (< 0.5 mM), high-sulphate (48 mg l-1 ) conditions in the organic-poor sandstone beneath the shale. These results indicated that active, phylogenetically diverse archaeal communities were present in the subsurface Cretaceous rock environment at this site and that major archaeal clades shifted dramatically over scales of tens of centimetres, corresponding to changes in the lithology and geochemical gradients. [ABSTRACT FROM AUTHOR]

Summary We characterized the diversity of sulphate-reducing bacteria (SRB) associated with South African gold mine boreholes and deep aquifer systems in Washington State, USA. Sterile cartridges filled with crushed country rock were installed on two hydrologically isolated and chemically distinct sites at depths of 3.2 and 2.7 km below the land surface (kmbls) to allow development of biofilms. Enrichments of sulphate-reducing chemolithotrophic (H2 ) and organotrophic (lactate) bacteria were established from each site under both meso- and thermophilic conditions. Dissimilatory sulphite reductase (Dsr) and 16S ribosomal RNA (rRNA) genes amplified from DNA extracted from the cartridges were most closely related to the Gram-positive species Desulfotomaculum thermosapovorans and Desulfotomaculum geothermicum , or affiliated with a novel deeply branching clade. The dsr sequences recovered from the Washington State deep aquifer systems affiliated closely with the South African sequences, suggesting that Gram-positive sulphate-reducing bacteria are widely distributed in the deep subsurface. [ABSTRACT FROM AUTHOR]

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Die Erzeugung von Elektrizität …… in hydrothermalen Strömungen unter dem Meeresboden beschreiben M. Yamamoto et al. in der Zuschrift auf S. 5819 ff. Die Ergebnisse belegen einen ausgedehnten und weiträumigen Elektronentransfer aus diesen hydrothermalen Strömungen zum Meeresboden über elektrisch leitfähige massive Mineralablagerungen. [ABSTRACT FROM AUTHOR]

Electricity generation is observed from sub‐seafloor hydrothermal fluids. In their Communication on page 5725 ff., M. Yamamoto et al. show widespread and distant electron transfer from sub‐seafloor hydrothermal fluids to the seafloor by way of electrically conductive massive hydrothermal mineral deposits. [ABSTRACT FROM AUTHOR]